Smoothing out mesh with holes
A couple of things you could do differently that will help...


Apply Rotation &amp; Scale before going into Edit Mode. That will keep your use of the Looptools > Circle from creating ovals.
Add an extra vertical edge loop in the middle of each section where you plan to put the holes.
Add an extra horizontal edge loop that cuts across all three hole areas.
THEN start doing the extrude/scale operation(s), followed by use of Looptools > Circle to create the holes.


Doing it this way will give you eight-sided holes which work out better in the long run.